EP4077728A4 - Methods and arrays for identifying the cell or tissue origin of dna - Google Patents

Methods and arrays for identifying the cell or tissue origin of dna Download PDF

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Publication number
EP4077728A4
EP4077728A4 EP20906917.8A EP20906917A EP4077728A4 EP 4077728 A4 EP4077728 A4 EP 4077728A4 EP 20906917 A EP20906917 A EP 20906917A EP 4077728 A4 EP4077728 A4 EP 4077728A4
Authority
EP
European Patent Office
Prior art keywords
arrays
dna
identifying
cell
methods
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
EP20906917.8A
Other languages
German (de)
French (fr)
Other versions
EP4077728A1 (en
Inventor
Yuval Ebenstein
Shahar ZIRKIN
Noa GILAT
Yael MICHAELI HOCH
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Ramot at Tel Aviv University Ltd
Original Assignee
Ramot at Tel Aviv University Ltd
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Ramot at Tel Aviv University Ltd filed Critical Ramot at Tel Aviv University Ltd
Publication of EP4077728A1 publication Critical patent/EP4077728A1/en
Publication of EP4077728A4 publication Critical patent/EP4077728A4/en
Pending legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6881—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/20—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Immunology (AREA)
  • Genetics & Genomics (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Pathology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Cell Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
EP20906917.8A 2019-12-22 2020-12-22 Methods and arrays for identifying the cell or tissue origin of dna Pending EP4077728A4 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201962952357P 2019-12-22 2019-12-22
PCT/IL2020/051320 WO2021130750A1 (en) 2019-12-22 2020-12-22 Methods and arrays for identifying the cell or tissue origin of dna

Publications (2)

Publication Number Publication Date
EP4077728A1 EP4077728A1 (en) 2022-10-26
EP4077728A4 true EP4077728A4 (en) 2024-05-22

Family

ID=76573848

Family Applications (1)

Application Number Title Priority Date Filing Date
EP20906917.8A Pending EP4077728A4 (en) 2019-12-22 2020-12-22 Methods and arrays for identifying the cell or tissue origin of dna

Country Status (4)

Country Link
US (1) US20230047930A1 (en)
EP (1) EP4077728A4 (en)
CA (1) CA3164738A1 (en)
WO (1) WO2021130750A1 (en)

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2023004204A2 (en) * 2021-07-23 2023-01-26 Georgetown University Use of circulating cell-free methylated dna to detect tissue damage

Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001049881A2 (en) * 2000-01-01 2001-07-12 Agrobiogen Gmbh Biotechnologie Dna matrices and the use thereof for examining individuals of a population
WO2004057026A1 (en) * 2002-12-23 2004-07-08 Indivumed Gmbh Multipatient cdna array in combination with a data collection
US20040203048A1 (en) * 2003-01-28 2004-10-14 Tran Nathaniel Tue High-throughput DNA methylation profiling and comparative analysis
US20080102450A1 (en) * 2006-10-26 2008-05-01 Barrett Michael T Detecting DNA methylation patterns in genomic DNA using bisulfite-catalyzed transamination of CpGS
WO2009134612A2 (en) * 2008-04-11 2009-11-05 University Of Utah Research Foundation Methods and compositions related to quantitative array based methylation analysis
US20100137154A1 (en) * 2008-12-01 2010-06-03 Ach Robert A Genome analysis using a methyltransferase
WO2017205827A1 (en) * 2016-05-26 2017-11-30 Singular Bio, Inc. Arrays for single molecule detection and uses thereof
WO2018178943A1 (en) * 2017-03-31 2018-10-04 Marcella Chiari Genotyping of mutations by combination of in-tube hybridization and universal tag-microarray

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20060292585A1 (en) * 2005-06-24 2006-12-28 Affymetrix, Inc. Analysis of methylation using nucleic acid arrays

Patent Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001049881A2 (en) * 2000-01-01 2001-07-12 Agrobiogen Gmbh Biotechnologie Dna matrices and the use thereof for examining individuals of a population
WO2004057026A1 (en) * 2002-12-23 2004-07-08 Indivumed Gmbh Multipatient cdna array in combination with a data collection
US20040203048A1 (en) * 2003-01-28 2004-10-14 Tran Nathaniel Tue High-throughput DNA methylation profiling and comparative analysis
US20080102450A1 (en) * 2006-10-26 2008-05-01 Barrett Michael T Detecting DNA methylation patterns in genomic DNA using bisulfite-catalyzed transamination of CpGS
WO2009134612A2 (en) * 2008-04-11 2009-11-05 University Of Utah Research Foundation Methods and compositions related to quantitative array based methylation analysis
US20100137154A1 (en) * 2008-12-01 2010-06-03 Ach Robert A Genome analysis using a methyltransferase
WO2017205827A1 (en) * 2016-05-26 2017-11-30 Singular Bio, Inc. Arrays for single molecule detection and uses thereof
WO2018178943A1 (en) * 2017-03-31 2018-10-04 Marcella Chiari Genotyping of mutations by combination of in-tube hybridization and universal tag-microarray

Non-Patent Citations (6)

* Cited by examiner, † Cited by third party
Title
CHUN-XIAO SONG ET AL: "Simultaneous single-molecule epigenetic imaging of DNA methylation and hydroxymethylation", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, vol. 113, no. 16, 19 April 2016 (2016-04-19), pages 4338 - 4343, XP055431116, ISSN: 0027-8424, DOI: 10.1073/pnas.1600223113 *
JOSHUA MOSS ET AL: "Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease", NATURE COMMUNICATIONS, vol. 9, no. 1, 1 December 2018 (2018-12-01), UK, XP055615527, ISSN: 2041-1723, DOI: 10.1038/s41467-018-07466-6 *
M. B. MILLER ET AL: "Basic Concepts of Microarrays and Potential Applications in Clinical Microbiology", CLINICAL MICROBIOLOGY REVIEW, vol. 22, no. 4, 1 October 2009 (2009-10-01), US, pages 611 - 633, XP055281490, ISSN: 0893-8512, DOI: 10.1128/CMR.00019-09 *
SAPIR MARGALIT ET AL: "5-Hydroxymethylcytosine as a clinical biomarker: Fluorescence-based assay for high-throughput epigenetic quantification in human tissues", INTERNATIONAL JOURNAL OF CANCER, JOHN WILEY & SONS, INC, US, vol. 146, no. 1, 2 July 2019 (2019-07-02), pages 115 - 122, XP071291141, ISSN: 0020-7136, DOI: 10.1002/IJC.32519 *
See also references of WO2021130750A1 *
SHEMA EFRAT ET AL: "Single-molecule decoding of combinatorially modified nucleosomes", SCIENCE, vol. 352, no. 6286, 6 May 2016 (2016-05-06), US, pages 717 - 721, XP093110131, ISSN: 0036-8075, DOI: 10.1126/science.aad7701 *

Also Published As

Publication number Publication date
WO2021130750A1 (en) 2021-07-01
US20230047930A1 (en) 2023-02-16
CA3164738A1 (en) 2021-07-01
EP4077728A1 (en) 2022-10-26

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